November 2013 - galaxy-user - lists.galaxyproject.org

bowtie2
by mark.rose＠syngenta.com 18 Nov '13

18 Nov '13

Hi All I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq files, Galaxy seems to recognize only one of the and places it in both inputs for paired end reads without any other options in the drop down menus. Thanks for your help Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Blast on Galaxy?
by Jorge Braun 18 Nov '13

18 Nov '13

hello users, 😊 My name is J.Braun and I am a new user of galaxy... It is a great tool for biologists. I have some questions and I would appreciate you could help me. 1) can I make a blast in Galaxy? 2) If so, can I download blast in galaxy? 3) If so, can I set up blast in my galaxy for analysis with only a particular species? Thank you very much

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Tophat/Cuff parameters
by Jennifer Jackson 17 Nov '13

17 Nov '13

Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name "-r", etc. To see all of the parameters on the forms: 1. Tophat/2 - open "TopHat settings to use: Full parameter list" 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed) so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy-dev(a)bx.psu.edu mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-user(a)bx.psu.edu mailing list going forward. Thanks, Jen Galaxy team On 11/14/13 1:08 PM, Irene Bassano wrote: > Hi Jen, > thanks a lot for your reply. > > I am trying to apply some changes to certain parameters in cufflinks. I have read them on the manual but on galaxy are not all listed. > is this because they have been chosen already by galaxy and set to certain values you guys believe are optimal? > I cannot find for example: > > Maximum genomic length allowed for a given bundle. > Minimum intron size allowed in genome. > Minimum average coverage required to attempt 3' trimming. > > and many others. > > I also wanted to access full parameters for Tophat and Cuffdiff... > > Any suggestion on how can I access them? > > Thanks, > Irene -- Jennifer Hillman-Jackson http://galaxyproject.org

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how to add openstack in biocloudcentral ?
by Zeeshan Ali Shah 15 Nov '13

15 Nov '13

Hi, I followed the guide from https://github.com/chapmanb/biocloudcentral and managed to run locally, But only see AWS in combo box, How to add private Openstack in it? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

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Cuffdiff question
by Jennifer Jackson 15 Nov '13

15 Nov '13

Hello, The transcript name when using RefSeq as a reference annotation is the "NM_" type of identifier. If you want to include a gene symbol, then the reference annotation should include the attribute "gene_name". The iGenomes GTF files are an example of datasets that include this attribute. http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See: /Example/?/*RNA-seq analysis*/*tools* http://cufflinks.cbcb.umd.edu/faq.html#gtfs http://cufflinks.cbcb.umd.edu/igenomes.html http://cufflinks.cbcb.umd.edu/manual.html (search on page for "gene_name" to see where can be used/output) Best, Jen Galaxy team On 11/12/13 10:40 AM, Irene Bassano wrote: > Dear Jennifer, > I am about to start a new analysis and learning from my old mistakes would like to ask just one question: > I would like my Cufflinks and Cuffdiff results to give me the actual gene name or transcript name rather than "NM_......" like I had last time i run the job. > > At which stage and which option do I have ti use to get the proper names? > > Thanks a lot! > > Irene -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org

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Setting a queue for torque submission
by Xian Su 14 Nov '13

14 Nov '13

Greetings I'm having a hard time getting job submission to work via torque. Posted below is the relevant part of my universe file and job_conf.xml. The main cause comes from our torque server requiring a queue to be requested. I can submit jobs just fine via job .sub files via command line using qsub -q M30 Running jobs via webgui results in the following: galaxy.jobs.runners.pbs WARNING 2013-11-14 13:54:23,722 (28) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations galaxy.jobs.runners.pbs ERROR 2013-11-14 13:54:25,724 (28) All attempts to submit job failed On the torque server's pbs logs, I see the corresponding 11/14/2013 13:54:23;0080;PBS_Server.66159;Req;req_reject;Reject reply code=15039(No default queue specified MSG=requested queue not found), aux=0, type=QueueJob, from xians(a)podmt1-100-62.novalocal In my universe_wsgi.ini, I'm currently using the settings: start_job_runners = pbs default_cluster_job_runner = pbs:///-q M30 -l nodes=1:ppn=12/ ^I mainly have no idea how to find the correct syntax for this pbs:/// But when I comment out default_cluster_job_runner and instead uncomment the line for the following job conf, I get the same error: <?xml version="1.0"?> <job_conf> <plugins workers="4"> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="pbs"> <destination id="local" runner="local"/> <destination id="pbs" runner="pbs" tags="mycluster"> <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=12</param> <param id="-q">M30</param> </destination> </destinations> <tools> <tool id="main" handler="main" destination="pbs"/> </tools> <limits> </limits> </job_conf> Thank you in advance for any help. Regards, Xian

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make publish histories only available to specific users
by mark.rose＠syngenta.com 13 Nov '13

13 Nov '13

Hello I am wondering whether it is possible to publish histories so that only certain users can see them. Histories that are published, rather than shared, appear to be more searchable. Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-user] Botryllus genome
by Enis Afgan 11 Nov '13

11 Nov '13

Hi Katie, For genomes that are not available on Galaxy Main (or general questions you might have about Galaxy), it's best to send an email to the galaxy-user mailing list (CC'd now). You can subscribe to the mailing list here http://lists.bx.psu.edu/listinfo/galaxy-user As far as the particular genome you're asking about, until it is to get added, you can upload it under your own account by following these instructions: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hope this helps, Enis On Sat, Nov 9, 2013 at 1:37 AM, Katie Marshall <kmarshall(a)zoology.ubc.ca>wrote: > Hi, > > I'm sorry to bother you, but I'm not entirely certain who to contact. I'm > starting up a project looking at gene transcription in Botryllus schlosseri > (a tunicate) that was recently genome-sequenced. I would love to have this > genome available through Galaxy, and currently under mapping tools it says > to "contact Galaxy Team" if my organism isn't listed. There's no link, so > if you could please pass me along to the appropriate person, that would be > fantastic. > > The NCBI listing for B. schlosseri is here: http://www.ncbi.nlm.nih.gov/ > bioproject/PRJNA205369 > > Cheers and thanks, > Katie > > -- > Dr. Katie Marshall > Postdoctoral Fellow > Department of Zoology > University of British Columbia > Room 138, Biodiversity Research Centre > 6270 University Blvd > Vancouver, BC > >

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Tophat2 (version 0.6)
by Roberta Galletti 08 Nov '13

08 Nov '13

Is there any chance to have the Arabidopsis genome put in the sliding menu of the Tophat2 (version 0.6)? Thank you Roberta Galletti

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How to lower disc usage in order to resume workflow
by Chris Farnet 08 Nov '13

08 Nov '13

Hello, Re: https://usegalaxy.org/u/cmfarnet/h/pf2-34-map-1-r1-only I am a new user, and I uploaded WGS data to perform the published "CloudMap Hawaiian Variant mapping with WGS" workflow (History link above). I received the notice: "You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota." Can you please let me know how I can reduce my disc usage so the the job can continue? Thanks so much for your help! Chris Farnet Dept. of Biology McGill University

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